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Gene: NMT2 |
Gene summary for NMT2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NMT2 | Gene ID | 9397 |
| Gene name | N-myristoyltransferase 2 | |
| Gene Alias | NMT2 | |
| Cytomap | 10p13 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | B3KT39 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 9397 | NMT2 | NAFLD1 | Human | Liver | NAFLD | 7.50e-08 | 7.26e-01 | -0.04 |
| 9397 | NMT2 | HCC1_Meng | Human | Liver | HCC | 8.08e-05 | -1.78e-01 | 0.0246 |
| 9397 | NMT2 | HCC2_Meng | Human | Liver | HCC | 1.47e-08 | -1.32e-01 | 0.0107 |
| 9397 | NMT2 | HCC1 | Human | Liver | HCC | 4.92e-22 | 4.41e+00 | 0.5336 |
| 9397 | NMT2 | HCC2 | Human | Liver | HCC | 1.25e-29 | 3.70e+00 | 0.5341 |
| 9397 | NMT2 | HCC5 | Human | Liver | HCC | 7.48e-19 | 2.84e+00 | 0.4932 |
| 9397 | NMT2 | Pt13.b | Human | Liver | HCC | 9.11e-04 | -1.66e-02 | 0.0251 |
| 9397 | NMT2 | Pt14.b | Human | Liver | HCC | 3.07e-02 | 1.74e-01 | 0.018 |
| 9397 | NMT2 | S014 | Human | Liver | HCC | 1.10e-02 | 2.50e-01 | 0.2254 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00160327 | Liver | NAFLD | viral process | 80/1882 | 415/18723 | 7.71e-09 | 1.07e-06 | 80 |
| GO:00190587 | Liver | NAFLD | viral life cycle | 57/1882 | 317/18723 | 1.00e-05 | 3.18e-04 | 57 |
| GO:00712145 | Liver | NAFLD | cellular response to abiotic stimulus | 56/1882 | 331/18723 | 7.01e-05 | 1.47e-03 | 56 |
| GO:01040045 | Liver | NAFLD | cellular response to environmental stimulus | 56/1882 | 331/18723 | 7.01e-05 | 1.47e-03 | 56 |
| GO:0043543 | Liver | NAFLD | protein acylation | 43/1882 | 243/18723 | 1.70e-04 | 3.07e-03 | 43 |
| GO:00714783 | Liver | NAFLD | cellular response to radiation | 33/1882 | 186/18723 | 8.76e-04 | 1.07e-02 | 33 |
| GO:001603222 | Liver | HCC | viral process | 286/7958 | 415/18723 | 4.41e-28 | 1.86e-25 | 286 |
| GO:001905822 | Liver | HCC | viral life cycle | 209/7958 | 317/18723 | 2.05e-17 | 2.09e-15 | 209 |
| GO:00435432 | Liver | HCC | protein acylation | 157/7958 | 243/18723 | 2.40e-12 | 1.12e-10 | 157 |
| GO:00421571 | Liver | HCC | lipoprotein metabolic process | 86/7958 | 135/18723 | 5.21e-07 | 8.38e-06 | 86 |
| GO:007121421 | Liver | HCC | cellular response to abiotic stimulus | 183/7958 | 331/18723 | 1.59e-06 | 2.26e-05 | 183 |
| GO:010400421 | Liver | HCC | cellular response to environmental stimulus | 183/7958 | 331/18723 | 1.59e-06 | 2.26e-05 | 183 |
| GO:00714782 | Liver | HCC | cellular response to radiation | 104/7958 | 186/18723 | 1.48e-04 | 1.19e-03 | 104 |
| GO:00421581 | Liver | HCC | lipoprotein biosynthetic process | 58/7958 | 96/18723 | 2.99e-04 | 2.13e-03 | 58 |
| GO:0044766 | Liver | HCC | multi-organism transport | 17/7958 | 21/18723 | 3.71e-04 | 2.56e-03 | 17 |
| GO:1902579 | Liver | HCC | multi-organism localization | 17/7958 | 21/18723 | 3.71e-04 | 2.56e-03 | 17 |
| GO:00064971 | Liver | HCC | protein lipidation | 55/7958 | 92/18723 | 6.12e-04 | 3.82e-03 | 55 |
| GO:0046794 | Liver | HCC | transport of virus | 15/7958 | 19/18723 | 1.36e-03 | 7.28e-03 | 15 |
| GO:00093146 | Liver | HCC | response to radiation | 223/7958 | 456/18723 | 3.08e-03 | 1.43e-02 | 223 |
| GO:0075733 | Liver | HCC | intracellular transport of virus | 9/7958 | 11/18723 | 9.51e-03 | 3.60e-02 | 9 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| NMT2 | SNV | Missense_Mutation | novel | c.100C>A | p.His34Asn | p.H34N | O60551 | protein_coding | tolerated_low_confidence(0.06) | benign(0.05) | TCGA-A8-A09N-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| NMT2 | SNV | Missense_Mutation | c.1415N>C | p.Gly472Ala | p.G472A | O60551 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| NMT2 | SNV | Missense_Mutation | c.1008N>C | p.Lys336Asn | p.K336N | O60551 | protein_coding | tolerated(0.08) | possibly_damaging(0.812) | TCGA-EW-A1P4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| NMT2 | insertion | In_Frame_Ins | novel | c.825_826insTCTAATAAGCATCCATTCAAA | p.Leu275_Glu276insSerAsnLysHisProPheLys | p.L275_E276insSNKHPFK | O60551 | protein_coding | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | ||
| NMT2 | deletion | Frame_Shift_Del | novel | c.728delA | p.Lys243ArgfsTer3 | p.K243Rfs*3 | O60551 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NMT2 | SNV | Missense_Mutation | rs765714868 | c.1211C>T | p.Thr404Met | p.T404M | O60551 | protein_coding | deleterious(0.01) | probably_damaging(0.99) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NMT2 | SNV | Missense_Mutation | c.1371N>C | p.Leu457Phe | p.L457F | O60551 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-FU-A5XV-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| NMT2 | SNV | Missense_Mutation | c.1356C>G | p.Phe452Leu | p.F452L | O60551 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-JW-A5VJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| NMT2 | SNV | Missense_Mutation | c.1087C>A | p.His363Asn | p.H363N | O60551 | protein_coding | tolerated(0.57) | benign(0.007) | TCGA-JW-A5VJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| NMT2 | SNV | Missense_Mutation | c.395N>C | p.Glu132Ala | p.E132A | O60551 | protein_coding | deleterious(0.03) | possibly_damaging(0.838) | TCGA-LP-A5U2-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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